Thursday, April 14, 2011

Casey Luskin Is Confused (Again)

The IDiots have painted themselves into a corner and they don't know what to do. They have been ranting against "Darwinism" for so long that they've come to believe that their silly version of evolution is what is being taught in the schools. When scientists objected to the "Darwinist" version of evolution the IDiots assumed that this was an objection to evolution. Gradually it seems to be dawning on them that there are legitimate scientific debates over the mechanisms of evolution and the relative contributions of various processes. These controversies have nothing to do with the FACTS of evolution.

But now the IDiots are in a bind. They can't retreat by admitting that their characterization of evolution has been wrong for the past few decades. That would make them look foolish. On the other hand, they can't continue to ignore the fact that major critics of "Darwinism" (or the "Modern Synthesis" or "Neo-Darwinism") are strong supporters of evolution and opponents of creationism, including Intelligent Design Creationism. Oops!

"elucidating the materialistic basis of the Cambrian explosion has become more elusive, not less, the more we know about the event itself, and cannot be explained away by coupling extinction of intermediates with long stretches of geologic time, despite the contrary claims of some modern neo-Darwinists" (McPeek)

"The edifice of the modern synthesis has crumbled, apparently, beyond repair" (Koonin)

But when their criticisms are cited by a proponent of intelligent design, they quickly toe the materialist party line, designed to reassure the masses that the paradigm has everything in order. Thus, when called upon by the NCSE to publicly defend the paradigm, Koonin eagerly endorses Dobzhansky's creed. As Newton eagerly boasted:

As the geneticist Theodosius Dobzhansky famously said - and as Eugene Koonin explicitly agreed - "Nothing in biology makes sense except in the light of evolution."

Since when do creeds take precedence over the evidence?

None of this, however, changes the fact that Koonin, McPeek, and many other scientists are writing technical papers stating that the neo-Darwinian model is flawed at its very core. Koonin undoubtedly believes Dobzhansky's statement is true, but I doubt he would say "Nothing in biology makes sense except in the light of neo-Darwinism." Why, then, must this model be taught to students as unadulterated fact?

Do you see the strategy? The IDiots are going to claim that their silly misunderstanding of evolution ("Darwinism" or "neo-Darwinism") is the "fact" of evolution that's being taught in the schools. Thus, it's not their fault that their understanding of evolution is wrong—blame it on the evolutionary biologists.

Yeah, that'll work! :-)

The alternative is to admit that the IDiots are, well .... idiots. Don't hold your breath waiting for that to happen.

I suppose we should be happy that they are finally beginning to see the very problem we've been telling them about for 25 years. They simply don't understand the real scientific version of evolution.

Speaking of those sidebar articles, Larry, I really wanted to read some of them for an article I am writing on genetic drift, but many of them have dead links. For example, your essays "Random genetic drift" and "Evolution by accident" go nowhere. It would be great to see these fixed.

To the Anonymous who asked about the real scientific version of evolution, science is not like religion: we do not have a sacred text and a single version of the truth. There is broad agreement on many aspects of evolution, but open debate about other aspects, as we should expect of an empirical science that is searching for truth. There really are a lot of good books about evolution in any university library which discuss these issues.

Dr. Moran posted:"I suppose we should be happy that they are finally beginning to see the very problem we've been telling them about for 25 years. They simply don't understand the real scientific version of evolution."

This means that for the last 25 years the "real scientific version of evolution" has been known.

What is that "real scientific version of evolution" that has been known for 25 years?

Luskin listed the 3 different meanings of the word "evolution":

"(1) Change over time (2) A grand tree of life (3) Natural selection acting on random mutations as primary driving force of adaptive change."

The only thing that has been known for 25 years is that things "change over time".

Moran:"Gradually it seems to be dawning on them that there are legitimate scientific debates over the mechanisms of evolution and the relative contributions of various processes. These controversies have nothing to do with the FACTS of evolution."

Anonymous, I cannot think of a single working biologist (one who regularly publishes in the scientific literature) who would disagree with Larry's statement:

"Here's one scientific FACT for you to chew on: humans and chimpanzees descend from a common ancestor that lived millions of years ago in Africa."

Long ago there were some scientists who thought the split between human and non-human primates occurred in Asia, but now the evidence is clear that it happened in Africa.

The common ancestry of chimps and humans is really undeniable, and people who do deny this are hard to take seriously on any other subject. Now that we have sequenced the genomes of both chimps and humans, the common descent is evident. That is why everyone who has worked on the subject, including fervent Bible-believing Christians like Francis Collins (who led the first human genome sequencing project), have no doubt about our common ancestry.

By the way, we could go further. There is virtually no doubt about:1. Common ancestry of all vertebrates.2. Common ancestry of all flowering plants.3. The orderly appearance of plants and animals in the fossil record, so that fossil assemblages become less like modern communities the deeper they are found. The deepest fossil assemblages contain no mammals, no vertebrate fish, no flowering plants. (The pattern expected under the hypothesis of a single creation event is the opposite of what we see. Under that hypothesis, we should see modern forms in the deepest deposits.)4. The great age of the earth (billions of years).5. The even greater age of the universe.

A point which you apparently either do not actually have or are embarrassed to make explicitly.

We run into these tactics so repeatedly, on this and so many other blogs. "Looks like you missed the point...." "You're obviously too stupid to understand what I was driving at...." But never explicitly making any point at all. It's so very transparent.

(1) "change over time" from common ancestry. Luskin keeps forgetting the last bit.

(2) "a grand tree of life" is only a graphic description of the consequences of descent with modification from common ancestry.

(3)"natural selection" is only one of a number of evolution mechanisms, it does not define evolution. I would note the sneaky phraseology used by Luskin, "adaptive change". Well yes, natural selection is a primary driving force for adaptive change. But adaptive change is not the only evolutionary process.

"Here's one scientific FACT for you to chew on: humans and chimpanzees descend from a common ancestor that lived millions of years ago in Africa."

Could you please tell us about this common ancestor? What are the characteristics? And most important what specific fossil evidence is there? Please indicate the fossils that were found, by whom they were found and where they were found. If it is a FACT, then there must be physical evidence. Right? Or is physical evidence not required for facts?

What are the characteristics? And most important what specific fossil evidence is there?

Please indicate the fossils that were found, by whom they were found and where they were found.

If it is a FACT, then there must be physical evidence. Right?

Or is physical evidence not required for facts?

Are genes physical? Last I looked they were. Want to explain the commonalities between the genomes if not from common ancestry?

Regarding fossils, here's what Wikipedia says:

There are no known fossils that represent the CHLCA [chimpanzee-human last common ancestor], so the age of the CHLCA is an estimate. The fossil find of Ardipithecus kadabba, Sahelanthropus tchadensis, and Orrorin tugenensis are closest in age and expected morphology of the CHLCA and suggest the LCA is older than 7 million years. [There's the answer to your question "What are the characteristics?"] Earliest studies of apes suggest the CHLCA may have been as old as 25 million years, however protein studies in the 1970s suggested the CHLCA was less than 8 million years in age. Genetic methods based on Orangutan/Human and Gibbon/Human LCA times have then been used to estimate Chimpanzee/Human LCA of 6 million years and LCA times between 5 and 7 million years are currently used in the literature.

So we haven't found fossils of the exact CHCLA yet, just as we haven't of Mitochondial Eve. It would be amazing if such a specific, ancient fossil actually were found. It would be like asking you to find the exact "second-best bed" that William Shakespeare willed to his wife, and that of course is many orders of magnitude more recent.

But even when fossil evidence has been found of "missing links" along the chain between chimps and humans (and there are many such), those who can't deal with the fact of evolution won't acknowledge their significance anyway.

I have a question that never seems to be addressed. Identifying the one particular individual last common ancestor is not really the issue. The issue is identifying the line of fossils from that particular individual. Is there a line of fossils leading from that unfound last common ancestor? Should there not be a set of individuals? But not one of that set has been found has it? Or has that lineage been found?

Unfortunately, the whole research on proximate mecahnisms (physiology etc.) is usually making sense without the slightest allusion to evolution. And part of the problem is, after all, that researchers of these quartiers can have a carriere without a proper understanding of evolutionary theory and become ID advocates in turn (see Michael Behe).

Joe

P.S.: Dobzhansky's quote is a statement about an "ought" rather than an "is".

The issue is identifying the line of fossils from that particular individual.

Is there a line of fossils leading from that unfound last common ancestor?

Should there not be a set of individuals?

But not one of that set has been found has it?

Or has that lineage been found?

The mistake is in thinking of a "line." There's a bush that forks at the last common ancestor (LCA); a couple of the branches off that fork eventually wind up as chimps and humans. Fossils that have been found which postdate the date range of the LCA may be from other branches off that fork (thus not part of the chimp or human lineage); they may be forks off one or the other of those branches (thus part of the lineage but not directly ancestral); or they may be on the branches themselves (thus directly ancestral). I hope you're still with me - if not, let me know. Sorry I'm no good at "ASCII art" or I'd try drawing you a picture.

Let's take Neanderthals as an example. As they've been studied, they've gone from being thought of as directly ancestral to being thought of primarily as a fork off the branch leading eventually to humans. With the latest genome research, it now appears that at least some small portion of their DNA has wound up in modern humans - i.e., there was some limited interbreeding between Neanderthals and the contemporary (more) direct human ancestors. So now that we've been able to do the DNA research - no easy task, and certainly not possible with all or even a majority of ancient hominid fossils of interest - we can answer the question of whether Neanderthals were directly ancestral to us by saying "Well, partially."

Being able to identify an LCA would involve finding very ancient bones and/or teeth with DNA sufficiently intact to show direct ancestry for both humans and chimps, and even then we'd have no real assurance it was the last such animal that exhibited such direct ancestry.

Identifying the precise LCA is a bit beside the point anyway, since genetic studies on humans, chimps, and other animals demonstrate to any reasonable individual beyond a shadow of a doubt that common ancestry is a feature of the species here on Earth. Thus there was an LCA that lived in a population of others of its species just as there was an individual Mitochondrial Eve who lived with others of her species, whether we manage to dig up the bones of those particular individuals or not. Even if we do dig up their bones, without testable DNA, there's no way to say "They're the ones," rather than more or less good candidates.

"But even when fossil evidence has been found of "missing links" along the chain between chimps and humans (and there are many such), those who can't deal with the fact of evolution won't acknowledge their significance anyway."

You are saying there is a chain from chimps to humans. Is that your position?

"The mistake is in thinking of a "line." There's a bush that forks at the last common ancestor (LCA); a couple of the branches off that fork eventually wind up as chimps and humans. Fossils that have been found which postdate the date range of the LCA may be from other branches off that fork (thus not part of the chimp or human lineage); they may be forks off one or the other of those branches (thus part of the lineage but not directly ancestral); or they may be on the branches themselves (thus directly ancestral). I hope you're still with me - if not, let me know. Sorry I'm no good at "ASCII art" or I'd try drawing you a picture. ETC."

My question is still the same and still unanswered. "Should there not be a set of individuals? But not one of that set has been found has it? Or has that lineage been found?"

Can anyone identify an actual fossil of an actual creature that is claimed to be an ancestor of modern chimps?

Can anyone identify an actual fossil of an actual creature that is claimed to be an ancestor of modern humans?

...and your question is still based on your incomplete and mistaken notions, so it will "remain unanswered" by reality. If you do get an answer, positive or negative, that is a signal the answer is not based on reality. The solution to your problem is not for someone to answer your question, but for you to read and learn more concerning the explanation I gave as to why you're asking the wrong question.

Here, I'll make it simpler, perhaps oversimplified:

- Yes, there are a group of individuals of a single species, among whom was the last common ancestor of chimps and humans.

- Finding fossils of this group is difficult and a crapshoot, like all fossils of such ancient vintage. But it is possible, and in fact such a fossil may already have been found.

- Determining through morphology whether a fossil, once found, is a potential candidate for LCA is possible. Such "potential candidates" have been found.

- Determining more exactly whether a fossil is of a creature in the lineage of both chimps and humans requires DNA testing. I don't know if any of the "potential candidate" fossils would have viable DNA to test. (I doubt any have so far - I think I would have read about it.) This, again, is a crapshoot.

- Determining scientifically whether a creature is in fact from the group containing the LCA is pretty much impossible, since there is always the chance of an undiscovered fossil of at least a few generations' more recent vintage, or that the actual LCA was from a group of slightly more recent individuals, none of whom wound up as fossils. (Fossils of that vintage are exceedingly rare, so it's strictly up to chance whether any individuals from the "right" population fossilized. As I keep saying, crapshoot.)

So: We may already have fossils from the group containing the LCA. But there's no way to be scientifically certain we have the "right" fossil.

Nevertheless, such an individual, genetically and mathematically, must have existed. It is equally as certain as the fact that you must have had great-great-great-great-great-great-great-great-great-great-grandparents, though chances of you knowing who they all were are minuscule. Your doubting the LCA existed is equally as wrongheaded as my doubting you had great-great-great-great-great-great-great-great-great-great-grandparents on the basis that you can't produce documentation. The question you are asking is equivalent to my demanding documentation proving who your great-great-great-great-great-great-great-great-great-great-grandparents were (though not exactly equivalent - there's a better chance you could produce the documentation, since it's of many orders of magnitude more recent vintage).

You need to read and learn about either the last common ancestor, mitochondrial Eve, or both, if your want to know why your question is based on an incomplete/incorrect understanding.

Well Jud is still pretending not to get it and try to overwhelm just by posting a lot of words.

There have been many fossils found and they have been categorized. Some are categorized as "sister taxon". But no fossil has ever been found which is actually on the claimed line that led to chimps nor any that is actually on the claimed line to humans. What I am saying is simply a fact. Nobody has ever found an actual fossil between the hypothetical (unfound) LCA and todays chimps or humans.

In fact there is no line. There is just a sudden appearance of the new creature type. That is what the fossil record shows. And Dr. Shapiro at the Univ of Chicago is showing out how that could happen.

"But even when fossil evidence has been found of "missing links" along the chain between chimps and humans (and there are many such), those who can't deal with the fact of evolution won't acknowledge their significance anyway."

You are saying there is a chain from chimps to humans. Is that your position?

Well Jud is still pretending not to get it and try to overwhelm just by posting a lot of words.

Thus you indicate both your continuing current lack of understanding (the "lot of words" I posted weren't very complicated at all, which indicates to me at least some degree of willful failure to understand on your part) and your lack of any motivation to do what I've been asking - learn something.

If you would bother to learn (it's not difficult - if I can, most folks certainly can), you'd figure out just how basic and elementary the misunderstanding behind your current question is. But I get the distinct impression that rather than endanger the invincible ignorance of your current position, you'd far rather characterize your own failure as a lack in evolutionary theory. That's fine - evolutionary theory won't suffer one bit, nor will I: I'm going to stop my obviously futile effort to cast bread upon the waters, having found in this case that the Bible verse most applicable is the one about pearls before swine.

"But even when fossil evidence has been found of "missing links" along the chain between chimps and humans (and there are many such), those who can't deal with the fact of evolution won't acknowledge their significance anyway."

You are saying there is a chain from chimps to humans. Is that your position?

Sorry to leave you all excited that maybe I wasn't "going to acknowledge" what I said.

Yep, I used the word "chain." It's not the best description of the actual relationship between us and chimps. The description I used in another comment was more accurate: If one thinks of a bush, the Last Common Ancestor of chimps and humans is at the junction of two twigs/branches. Chimps are on one branch and humans are on the other. The relationship is still an extremely close one, though, as the commonalities between the genomes show.

Poor Jud. He keeps getting caught.Not only is he now claiming a chain (or not) but he actually has humans evolving from chimps. Notice his reference to the chain of creatures "between chimps and humans".

And yet he gamely maintains his supercilious attitude in the face of all this.

But this is all a distraction anyway, since there is no line of found fossils between the LCA and any of these creatures. As the fossil record shows, there is just the sudden appearance of the new creature types.

But this is all a distraction anyway, since there is no line of found fossils between the LCA and any of these creatures. As the fossil record shows, there is just the sudden appearance of the new creature types.

http://en.wikipedia.org/wiki/Punctuated_equilibrium

"Punctuated equilibrium (also called punctuated equilibria) is a theory in evolutionary biology which proposes that most sexually reproducing species will experience little net evolutionary change for most of their geological history, remaining in an extended state called stasis. Punctuated equilibrium also proposes that stasis is broken up by rare and rapid events of branching speciation called cladogenesis. Cladogenesis is the process by which species split into two distinct species, rather than one species gradually transforming into another."

I attempted to read Dr. Shapiro's 2009 (Ann N Y Acad Sci. 2009 Oct;1178:6-28). After reading the paper, it's impossible for me to become that impressed by his "theory". He spends the paper attacking false statements about what modern biology thinks. In every instance he is incorrect on what modern biologists actually think, and is attacking concepts not held by anyone I work with.

He also over-inflates the importance of things like epigenetics, and the claims about whole genome transcription (boy those salamanders must be really complex!).

the other Jim posted:"But this is all a distraction anyway, since there is no line of found fossils between the LCA and any of these creatures. As the fossil record shows, there is just the sudden appearance of the new creature types."

http://en.wikipedia.org/wiki/Punctuated_equilibrium

"Punctuated equilibrium (also called punctuated equilibria) is a theory in evolutionary biology which proposes that most sexually reproducing species will experience little net evolutionary change for most of their geological history, remaining in an extended state called stasis. Punctuated equilibrium also proposes that stasis is broken up by rare and rapid events of branching speciation called cladogenesis. Cladogenesis is the process by which species split into two distinct species, rather than one species gradually transforming into another."

You mean saying a term I used in a blog comment wasn't the best word to describe the reality? It's called being duly humble and straightforward. Try it sometime.

Not only is he now claiming a chain (or not) but he actually has humans evolving from chimps.

Notice his reference to the chain of creatures "between chimps and humans".

So you crow about my statement saying "chain" was the wrong word to use, then go on about my claiming there's a "chain"? How very disingenuous.

the other Jim seems to understand what I am saying.

So you now agree there was a Last Common Ancestor of chimps and humans? Because I guarantee you the other Jim isn't arguing with that proposition one iota, nor does the theory of punctuated equilibrium contradict that fact in any way.

So will you do what I did and say you perhaps did not express yourself correctly in your past statements? Or do you lack the humility and honesty to do so?

Or is it (more likely, I'd guess) that you have no least idea how punctuated equilibrium actually fits into a discussion of the Last Common Ancestor?

Ooh, can I guess? Perhaps 'cause it looks like you're trying to use Punctuated Equilibrium to question common ancestry, and as Larry commented earlier in this thread:

Here's one scientific FACT for you to chew on: humans and chimpanzees descend from a common ancestor that lived millions of years ago in Africa.

If you don't accept that as a scientific fact then you don't accept science.

If you are not questioning common ancestry, then your last 10 or so comments in this thread are a remarkably incoherent way of expressing that. (But of course your attempt to use punctuated equilibrium as an objection to common ancestry is an incoherent argument as well, so who can guess which way you have chosen to be nonsensical?)

Jud is doing his best to avoid admitting that he spoke of humans evolving from chimps and not both evolving from a common ancestor.

I'm quite sure anyone with rudimentary reading comprehension skills looking at my comments in this thread easily understands what I'm saying about common ancestry. Yet after 5 comments specifically about this, you apparently still haven't got it. Oh, but I did specify rudimentary reading comprehension.

But it is tiresome to keep correcting him.

Why stop at a mere 5 comments? I bet you could keep from having to say anything at all about your own "understanding" of punctuated equilibrium, common ancestry, etc., virtually forever if you just keep banging away at this "chain" business.

C'mon, Anonymous, inquiring minds want to know - how does punctuated equilibrium relate to the Last Common Ancestor?

Laurence A. Moran

Larry Moran is a Professor in the Department of Biochemistry at the University of Toronto. You can contact him by looking up his email address on the University of Toronto website.

Sandwalk

The Sandwalk is the path behind the home of Charles Darwin where he used to walk every day, thinking about science. You can see the path in the woods in the upper left-hand corner of this image.

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Quotations

The old argument of design in nature, as given by Paley, which formerly seemed to me to be so conclusive, fails, now that the law of natural selection has been discovered. We can no longer argue that, for instance, the beautiful hinge of a bivalve shell must have been made by an intelligent being, like the hinge of a door by man. There seems to be no more design in the variability of organic beings and in the action of natural selection, than in the course which the wind blows.Charles Darwin (c1880)Although I am fully convinced of the truth of the views given in this volume, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed, during a long course of years, from a point of view directly opposite to mine. It is so easy to hide our ignorance under such expressions as "plan of creation," "unity of design," etc., and to think that we give an explanation when we only restate a fact. Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject the theory.

Charles Darwin (1859)Science reveals where religion conceals. Where religion purports to explain, it actually resorts to tautology. To assert that "God did it" is no more than an admission of ignorance dressed deceitfully as an explanation...

Quotations

The world is not inhabited exclusively by fools, and when a subject arouses intense interest, as this one has, something other than semantics is usually at stake.
Stephen Jay Gould (1982)
I have championed contingency, and will continue to do so, because its large realm and legitimate claims have been so poorly attended by evolutionary scientists who cannot discern the beat of this different drummer while their brains and ears remain tuned to only the sounds of general theory.
Stephen Jay Gould (2002) p.1339
The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies raw material only. Natural selection directs the course of evolutionary change.
Stephen Jay Gould (1977)
Rudyard Kipling asked how the leopard got its spots, the rhino its wrinkled skin. He called his answers "just-so stories." When evolutionists try to explain form and behavior, they also tell just-so stories—and the agent is natural selection. Virtuosity in invention replaces testability as the criterion for acceptance.
Stephen Jay Gould (1980)
Since 'change of gene frequencies in populations' is the 'official' definition of evolution, randomness has transgressed Darwin's border and asserted itself as an agent of evolutionary change.
Stephen Jay Gould (1983) p.335
The first commandment for all versions of NOMA might be summarized by stating: "Thou shalt not mix the magisteria by claiming that God directly ordains important events in the history of nature by special interference knowable only through revelation and not accessible to science." In common parlance, we refer to such special interference as "miracle"—operationally defined as a unique and temporary suspension of natural law to reorder the facts of nature by divine fiat.
Stephen Jay Gould (1999) p.84

Quotations

My own view is that conclusions about the evolution of human behavior should be based on research at least as rigorous as that used in studying nonhuman animals. And if you read the animal behavior journals, you'll see that this requirement sets the bar pretty high, so that many assertions about evolutionary psychology sink without a trace.

Jerry Coyne
Why Evolution Is TrueI once made the remark that two things disappeared in 1990: one was communism, the other was biochemistry and that only one of them should be allowed to come back.

Sydney Brenner
TIBS Dec. 2000
It is naïve to think that if a species' environment changes the species must adapt or else become extinct.... Just as a changed environment need not set in motion selection for new adaptations, new adaptations may evolve in an unchanging environment if new mutations arise that are superior to any pre-existing variations

Douglas Futuyma
One of the most frightening things in the Western world, and in this country in particular, is the number of people who believe in things that are scientifically false. If someone tells me that the earth is less than 10,000 years old, in my opinion he should see a psychiatrist.

Francis Crick
There will be no difficulty in computers being adapted to biology. There will be luddites. But they will be buried.

Sydney Brenner
An atheist before Darwin could have said, following Hume: 'I have no explanation for complex biological design. All I know is that God isn't a good explanation, so we must wait and hope that somebody comes up with a better one.' I can't help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist

Richard Dawkins
Another curious aspect of the theory of evolution is that everybody thinks he understand it. I mean philosophers, social scientists, and so on. While in fact very few people understand it, actually as it stands, even as it stood when Darwin expressed it, and even less as we now may be able to understand it in biology.

Jacques Monod
The false view of evolution as a process of global optimizing has been applied literally by engineers who, taken in by a mistaken metaphor, have attempted to find globally optimal solutions to design problems by writing programs that model evolution by natural selection.